The story was meant as a sort of "new start" for the character—to redefine him from his origins as an arms dealer, to be the "test pilot for the future" Ellis intended him to be.

Miles underground in his Coney Island "garage", Stark is awakened from sleep and several weeks of work, isolation, and diminished self care by his secretary's phone call, reminding him of a scheduled interview with a journalist.

During the interview, it emerges that Stark deeply regrets that the world-changing, humanitarian improvements he had hoped to fund with his weapons sales have not yet materialized.

Confronted by his regrets, Stark returns to the garage, takes stock of himself while realizing that the Iron Man is likely his key to a better future for both himself and humanity.

Having canceled all appointments, Tony Stark dons the newest version of the Iron Man armor and takes off into the sky.

Meanwhile, the injected man's body, still lying in the Bastrop warehouse, is now covered completely in a bizarre layer of scar tissue.

The note informs co-worker Maya Hansen that he has stolen and "loosed" the company's dangerous Extremis serum for some "greater" purpose.

Stark arrives in Texas in the middle of a teleconference with his board of directors, rejecting their requests that he resign as CEO of his company and take a head technician title instead.

Tony also argues that Stark Industries, having invented a revolutionary cell phone and connection method, no longer needs the government's funding.

Arriving at Futurepharm, Stark learns that the intended receiver of the Extremis dose is currently unknown due to an inability to hack Killian's computer.

Using Stark Industry's new prototype phone, Tony emails Killian's entire hard drive to be hacked by one of his employees, and, to distract Maya, jets her and himself to San Diego to talk with their old friend and teacher, Sal Kennedy.

While Kennedy, now a futurist following nature and an idealistic way of life, harangues Tony and Maya on their military work and thus-far-failed promise, Mallen sets the FBI office on fire using his new biological powers.

Iron Man tracks the terrorists' van from above via body heat scans and tears it in half with a non-lethal repulsor ray.

Suffering severe injuries and damage to his armor, Iron Man and the police manage to repulse Mallen, though civilian casualties are present.

Knowing the severity of his injuries, Tony realizes the only way for him to survive and defeat Mallen is to become one with the Iron Man suit by taking the Extremis serum himself.

Unknown to Maya, Tony had altered the structure of the Extremis dose, removing several safeties and linking himself to his armor and machinery.

While unconscious, Stark relives his story as Iron Man, starting with his first mortal injury and the secrets he revealed to Yinsen while they constructed the original Arc Reactor (used to still the shrapnel lodged in Stark's chest and prevent it from puncturing his heart) and Iron Man suit (something powered by the same thing keeping him alive that would allow for the two of them to escape their captors).

An internal control sheath for his Iron Man armor is now contained within the hollows of his bones, able to emerge upon mental command.

Tapping into a satellite cluster, Iron Man finds Mallen heading towards Washington, intent on killing the president.

But Mallen retained said super-powers, resulting in his high-level super-strength, super-speed, advanced invulnerability, and the abilities to breathe fire and project arcs of electricity from his hands, as well as being bullet-proof.

These hallucinations served to make him aware of facts that he had noted subconsciously while not recognizing their relevance or existence on a conscious level, such as that a member of the Initiative had lied about his powers (he claimed to just have superhuman physical abilities when he actually manipulated gravity to create the appearance of superstrength, as otherwise he couldn't be given an IV while in hospital as he would have had invulnerable skin), or that Maya Hansen was actually alive after her death was faked.

Doc Samson speculated that the hallucinations appeared because the excess information was filtered into the same place Stark subconsciously stored his guilt to stop himself facing it.

[14] During the 2010 "Stark: Disassembled" storyline, Tony is forced to erase portions of his memory in order to prevent Norman Osborn from gaining access to the list of people registered under the Superhuman Registration Act.

[16] During the 2012 "Believe" story arc, Tony learns that Maya Hansen has been killed and various new versions of Extremis have been released onto the black market, prompting him to track them down and eliminate them.

he created to facilitate his efforts at finding a cure has begun to work against him by using more Maestro-esque tactics,[25] with Doc Green declining the option of a new Extremis upgrade for fear of becoming a new Maestro.

He experienced a new surge of his more negative traits such as his ego, irresponsibility, and alcoholism, culminating in him releasing a new version of Extremis onto San Francisco.

[28] Daredevil subsequently realized that Stark had added the Extremis virus to San Francisco's water supply, with the phones simply transmitting a subsonic signal that activated the already-existing virus in their bodies, but Stark subjected Matt to minor brain damage to erase his memories of this discovery, intending to reprogram the activation signal to a frequency Daredevil cannot detect.

Based on his work on the story arc, artist Adi Granov was brought on as a producer for the film,[6] who went on to create the final designs for Iron Man's armor.

In "Girl in the Flower Dress", Project Centipede attempts to improve the serum by experimenting on pyrokinetic street performer Chan Ho Yin; during which they harvest his blood platelets to stabilize Extremis' unstable elements.